[2024-01-25 19:56:20,366] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:20,372] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:20,372] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b149d2d-0b68-410e-8e80-f716d1aa4a81/dqc_reference
[2024-01-25 19:56:21,587] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:21,588] [INFO] Task started: Prodigal
[2024-01-25 19:56:21,588] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f0d9852-479d-4eca-94d2-7b7e933b6e59/GCF_900128475.1_PRJEB18047_genomic.fna.gz | prodigal -d GCF_900128475.1_PRJEB18047_genomic.fna/cds.fna -a GCF_900128475.1_PRJEB18047_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:40,895] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:40,896] [INFO] Task started: HMMsearch
[2024-01-25 19:56:40,896] [INFO] Running command: hmmsearch --tblout GCF_900128475.1_PRJEB18047_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b149d2d-0b68-410e-8e80-f716d1aa4a81/dqc_reference/reference_markers.hmm GCF_900128475.1_PRJEB18047_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:41,151] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:41,152] [INFO] Found 6/6 markers.
[2024-01-25 19:56:41,189] [INFO] Query marker FASTA was written to GCF_900128475.1_PRJEB18047_genomic.fna/markers.fasta
[2024-01-25 19:56:41,189] [INFO] Task started: Blastn
[2024-01-25 19:56:41,189] [INFO] Running command: blastn -query GCF_900128475.1_PRJEB18047_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b149d2d-0b68-410e-8e80-f716d1aa4a81/dqc_reference/reference_markers.fasta -out GCF_900128475.1_PRJEB18047_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:41,779] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:41,782] [INFO] Selected 24 target genomes.
[2024-01-25 19:56:41,782] [INFO] Target genome list was writen to GCF_900128475.1_PRJEB18047_genomic.fna/target_genomes.txt
[2024-01-25 19:56:41,792] [INFO] Task started: fastANI
[2024-01-25 19:56:41,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f0d9852-479d-4eca-94d2-7b7e933b6e59/GCF_900128475.1_PRJEB18047_genomic.fna.gz --refList GCF_900128475.1_PRJEB18047_genomic.fna/target_genomes.txt --output GCF_900128475.1_PRJEB18047_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:58,389] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:58,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b149d2d-0b68-410e-8e80-f716d1aa4a81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:58,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b149d2d-0b68-410e-8e80-f716d1aa4a81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:58,403] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:56:58,403] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:56:58,403] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	81.6606	248	1305	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	79.9562	370	1305	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	79.7341	76	1305	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	79.6947	210	1305	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	79.2973	368	1305	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	79.1914	373	1305	95	below_threshold
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	79.1819	367	1305	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	79.1755	386	1305	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	79.168	364	1305	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	79.0967	399	1305	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	79.0854	223	1305	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	79.063	356	1305	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	79.0351	351	1305	95	below_threshold
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	78.9393	408	1305	95	below_threshold
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	78.9105	353	1305	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	78.8474	362	1305	95	below_threshold
Bacteroides oleiciplenus	strain=YIT 12058	GCA_000315485.1	626931	626931	type	True	78.5955	269	1305	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	78.5861	300	1305	95	below_threshold
Bacteroides congonensis	strain=Marseille-P3132	GCA_900130125.1	1871006	1871006	type	True	78.2316	204	1305	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	78.1472	101	1305	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	78.0725	102	1305	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	77.8835	137	1305	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_002959715.1	47678	47678	suspected-type	True	77.818	142	1305	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.8233	87	1305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:58,405] [INFO] DFAST Taxonomy check result was written to GCF_900128475.1_PRJEB18047_genomic.fna/tc_result.tsv
[2024-01-25 19:56:58,405] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:58,405] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:58,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b149d2d-0b68-410e-8e80-f716d1aa4a81/dqc_reference/checkm_data
[2024-01-25 19:56:58,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:58,446] [INFO] Task started: CheckM
[2024-01-25 19:56:58,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900128475.1_PRJEB18047_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900128475.1_PRJEB18047_genomic.fna/checkm_input GCF_900128475.1_PRJEB18047_genomic.fna/checkm_result
[2024-01-25 19:57:52,390] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:52,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:52,412] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:52,412] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:52,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900128475.1_PRJEB18047_genomic.fna/markers.fasta)
[2024-01-25 19:57:52,414] [INFO] Task started: Blastn
[2024-01-25 19:57:52,414] [INFO] Running command: blastn -query GCF_900128475.1_PRJEB18047_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b149d2d-0b68-410e-8e80-f716d1aa4a81/dqc_reference/reference_markers_gtdb.fasta -out GCF_900128475.1_PRJEB18047_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:53,451] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:53,454] [INFO] Selected 14 target genomes.
[2024-01-25 19:57:53,454] [INFO] Target genome list was writen to GCF_900128475.1_PRJEB18047_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:53,463] [INFO] Task started: fastANI
[2024-01-25 19:57:53,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f0d9852-479d-4eca-94d2-7b7e933b6e59/GCF_900128475.1_PRJEB18047_genomic.fna.gz --refList GCF_900128475.1_PRJEB18047_genomic.fna/target_genomes_gtdb.txt --output GCF_900128475.1_PRJEB18047_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:03,506] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:03,515] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:03,515] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900128475.1	s__Bacteroides massiliensis	100.0	1303	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	conclusive
GCA_019116805.1	s__Bacteroides merdavium	86.5638	663	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130135.1	s__Bacteroides togonis	86.1711	768	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.34	96.94	0.82	0.80	8	-
GCF_900108345.1	s__Bacteroides ndongoniae	82.083	611	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	97.32	0.85	0.83	4	-
GCA_905201685.1	s__Bacteroides sp905201685	80.4918	234	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553815.1	s__Bacteroides sp900553815	79.9616	374	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.95	97.95	0.73	0.73	2	-
GCA_019118325.1	s__Bacteroides intestinavium	79.6174	352	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154205.1	s__Bacteroides uniformis	79.2943	369	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCA_017471925.1	s__Bacteroides sp017471925	79.2885	353	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883785.1	s__Bacteroides intestinipullorum	79.2873	311	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154525.1	s__Bacteroides stercoris	78.979	358	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_900291465.1	s__Phocaeicola_A sp900291465	78.6643	248	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola_A	95.0	97.97	97.87	0.87	0.85	4	-
GCF_004342845.1	s__Bacteroides heparinolyticus	78.4337	292	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	-
GCA_905203765.1	s__Bacteroides sp905203765	78.172	259	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:03,517] [INFO] GTDB search result was written to GCF_900128475.1_PRJEB18047_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:03,518] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:03,521] [INFO] DFAST_QC result json was written to GCF_900128475.1_PRJEB18047_genomic.fna/dqc_result.json
[2024-01-25 19:58:03,521] [INFO] DFAST_QC completed!
[2024-01-25 19:58:03,521] [INFO] Total running time: 0h1m43s